Fluorescent dyes have many uses and are known to be particularly suitable for biological applications in which the high detectability of fluorescence is desirable. By binding to a specific biological ingredient in a sample, a fluorescent dye can be used to indicate the presence or the quantity of the specific ingredient in a sample. A variety of fluorescent dyes are available for specific fluorescent staining and quantitation of DNA and RNA, and other applications involving nucleic acids.
Unsymmetrical cyanine dyes were described long before much was known about DNA, by Brooker, et al., J. AM. CHEM. SOC. 64, 199 (1942). Some dyes in this class have since been found to be useful in fluorescent staining of DNA and RNA. The dye sold under the name Thiazole Orange has particular advantages in the quantitative analysis of immature blood cells or reticulocytes. U.S. Pat. No. 4,883,867 to Lee, et al. (1989) ('867 patent); Lee, et al., Thiazole Orange: A New Dye for Reticulocyte Analysis, CYTOMETRY 7, 508 (1986). As indicated in the '867 patent to Lee, et al., the dye used for this purpose must be able to penetrate the cell membrane.
The inventors have discovered that a composition that includes a side chain with additional positive charges is a polar compound that is unable to readily penetrate cell membranes. Nevertheless, the dye discovered by inventors is highly useful as a stain for nucleic acids because it has an extremely high affinity for nucleic acid polymers that is greater than that of the parent compounds (e.g. thiazole orange, oxazole yellow, thiazole red). The dyes of the invention are sensitive to even small quantities of nucleic acid polymers not contained inside living cells, e.g. in cell extracts, as well as to nucleic acids in permeabilized cells, such as dead or fixed cells. The combination of dye with nucleic acid polymers generally results in fluorescence that is linearly related to the amount of polymer present in the sample.
The novel fluorescent dyes is similar to another discovery of inventors, DIMERS OF UNSYMMETRICAL CYANINE DYES (Ser. No. 07/761,177 filed Sep. 16, 1991 by Yue, Johnson & Haugland). The dimer compounds contain two unsymmetrical cyanine dye units linked by a bridge having one or more positive charges, whereas the monomer dyes of the instant invention contain only one unsymmetrical cyanine dye unit. The affinity of the dimer for nucleic acid polymers is even greater than that of the subject invention. For some applications high affinity may cause problems where removal of the dye to allow recovery of the nucleic acid polymers is desired. It is advantageous to have a dye that has an affinity for nucleic acids that is not so strong as to require harsh conditions to separate the bound dye from the nucleic acid, yet is strong enough to permit rapid binding to and quantitative detection of the polymer, with minimum background from unbound dye. In addition, the monomer dye with cationic side chain unexpectedly shows less optical deterioration in aqueous solutions than the dimer. This characteristic of the monomer dyes in aqueous solutions is advantageous in that the dye continues to be useful in the evaluation of nucleic acids even under prolonged experimental conditions.